Locus 12442

Sequence ID	dm3.chrXHet
Location	203,355 – 203,543
Length	188
Max. P	0.996726

overview

Window 2

Location	203,355 – 203,448
Length	93
Sequences	4
Columns	93
Reading direction	forward
Mean pairwise identity	63.06
Shannon entropy	0.62070
G+C content	0.57832
Mean single sequence MFE	-38.70
Consensus MFE	-16.20
Energy contribution	-17.70
Covariance contribution	1.50
Combinations/Pair	1.39
Mean z-score	-2.64
Structure conservation index	0.42
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.98
SVM RNA-class probability	0.996726
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 203355 93 + 204112
GUGCGGACGAUGGUUGCACCCUCCCUCGGAGUCAGAGUACACGAGGUACGUGAGCUCCGUCGAGGUGGUGGUGCGAUCAUUCGUACUCCUUCG
(((((...(((((((((((((..((((((.....((((.((((.....)))).))))..))))))..).)))))))))))))))))....... ( -44.30, z-score =  -3.30, R)
>dp4.Unknown_singleton_2130 3913 90 + 5907
GUUGUGAAAGAGGUGGGGCCAUCCUUGGGGGUGCGCAUACUUGAGGU---UAAGCCUCGCCGUGAUGGUAGUGUGAUUAUUCGCACUCCAUCU
...........((((((((...(((..((.(....)...))..))).---...))))))))..(((((.(((((((....)))))))))))). ( -40.80, z-score =  -4.06, R)
>droPer1.super_92 115677 90 - 190782
GUCAAGAAGACCGUGGUGCCGACACUUGGAGUCCGCGUCCACGAGGCUCGCGAGCUG---AAGAGCGGAGGAGCGAUUAUUCGCACCCCUUCA
(((.....)))((((((((.(((.......))).))).)))))..((((........---..))))(((((.((((....))))...))))). ( -32.50, z-score =  -0.75, R)
>droGri2.scaffold_15056 30690 90 - 38174
GUAGUGAAGGAGGUAGGGCCUACCUUAGGUGUGCGCGUCCAUGAGGU---GAAACCUCUGCGGGAUGGUGGAGCGAUCAUUCGCACACCAUCU
((((..(((((((.....))).))))((((...(((.((...)).))---)..)))))))).((((((((..((((....)))).)))))))) ( -37.20, z-score =  -2.44, R)
>consensus
GUAGUGAAGAAGGUGGGGCCAACCCUAGGAGUCCGCGUACACGAGGU___UAAGCCUCG_CGGGAUGGUGGAGCGAUCAUUCGCACUCCAUCU
............((((..((.......))...))))......(((((......))))).....(((((.(((((((....)))))))))))). (-16.20 = -17.70 +   1.50)

alignment

secondary structure

dotplot

Window 3

Location	203,390 – 203,488
Length	98
Sequences	4
Columns	98
Reading direction	forward
Mean pairwise identity	63.08
Shannon entropy	0.60299
G+C content	0.52994
Mean single sequence MFE	-32.30
Consensus MFE	-20.10
Energy contribution	-20.22
Covariance contribution	0.12
Combinations/Pair	1.48
Mean z-score	-1.49
Structure conservation index	0.62
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.28
SVM RNA-class probability	0.987473
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 203390 98 + 204112
AGUACACGAGGUACGUGAGCUCCGUCGAGGUGGUGGUGCGAUCAUUCGUACUCCUUCGGUUGGAGAGCUGCAGAAGGUGAUGGCAUCGAAAAGAUUCG
..(((.(((((..(....)..)).)))..))).((((((.((((((((((((((.......))))...))).))..))))).)))))).......... ( -27.60, z-score =   0.72, R)
>dp4.Unknown_singleton_2130 3948 95 + 5907
CAUACUUGAGGU---UAAGCCUCGCCGUGAUGGUAGUGUGAUUAUUCGCACUCCAUCUGUUGCCGAGCGGAAGAAAAUUGCGGAAAAUGCAAAGUUUG
((.((((((((.---....)))).(((..((((.(((((((....))))))))).((((((....)))))).....))..)))........)))).)) ( -32.20, z-score =  -3.17, R)
>droPer1.super_92 115712 95 - 190782
CGUCCACGAGGCUCGCGAGCU---GAAGAGCGGAGGAGCGAUUAUUCGCACCCCUUCAGUGAGCGAACUGAGGAAGGUAGUGGCCAGCAGCAAAUUUA
.(.((((...((((((..(((---....)))(((((.((((....))))...))))).))))))..(((......))).)))).)............. ( -31.20, z-score =  -0.70, R)
>droGri2.scaffold_15056 30725 95 - 38174
CGUCCAUGAGGU---GAAACCUCUGCGGGAUGGUGGAGCGAUCAUUCGCACACCAUCUGUUGCCGAGCGGAAGAAGAUUGCGGGGAACGCAAAAUUCA
..(((..((((.---....)))).(((((((((((..((((....)))).))))))))..))).....))).(((..(((((.....)))))..))). ( -38.20, z-score =  -2.80, R)
>consensus
CGUACACGAGGU___UAAGCCUCGGCGGGAUGGUGGAGCGAUCAUUCGCACUCCAUCUGUUGCCGAGCGGAAGAAGAUUGCGGCAAACACAAAAUUCA
.......(((((......)))))........((.(((((((....))))))))).(((((......))))).(((..(((((.....)))))..))). (-20.10 = -20.22 +   0.12)

alignment

secondary structure

dotplot

Window 4

Location	203,412 – 203,528
Length	116
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	57.16
Shannon entropy	0.70119
G+C content	0.51507
Mean single sequence MFE	-32.79
Consensus MFE	-16.38
Energy contribution	-16.38
Covariance contribution	0.00
Combinations/Pair	1.45
Mean z-score	-1.30
Structure conservation index	0.50
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.92
SVM RNA-class probability	0.974858
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 203412 116 + 204112
CGUCGAGGUGGUGGUGCGAUCAUUCGUACUCCUUCGGUUGGAGAGCUGCAGAAGGUGAUGGCAUCGAAAAGAUUCGCAGAACUUGGACUGAAUGUGGCACGGAACGCGGCCGAGAA
..((..(((.(((((((((....))))))((((((((((.(((..((((....((((....))))(((....)))))))..))).))))))).(.....)))).))).)))..)). ( -41.50, z-score =  -1.49, R)
>dp4.Unknown_singleton_2130 3974 99 + 5907
-------AUGGUAGUGUGAUUAUUCGCACUCCAUCUGUUGCCGAGCGGAAGAAAAUUGCGGAAAAUGCAAAGUUUGAUGAGGUAGGACUGACUGUGAAGGUCAAUG----------
-------((((.(((((((....)))))))))))...(((((...((...(((..(((((.....)))))..)))..)).)))))...(((((.....)))))...---------- ( -28.40, z-score =  -2.09, R)
>droPer1.super_92 115734 103 - 190782
---AAGAGCGGAGGAGCGAUUAUUCGCACCCCUUCAGUGAGCGAACUGAGGAAGGUAGUGGCCAGCAGCAAAUUUACCGAAGCAGGACUGGAGGUUAAGAAGAGUC----------
---.........((.((((....)))).))((((((((.......(((.....(((((..((.....))....)))))....))).))))))))............---------- ( -26.00, z-score =  -0.10, R)
>droGri2.scaffold_15056 30747 113 - 38174
---CGGGAUGGUGGAGCGAUCAUUCGCACACCAUCUGUUGCCGAGCGGAAGAAGAUUGCGGGGAACGCAAAAUUCAGCGAAGUUGGUCUGGAAGUGAGUGUGAAAGAGAGACUGGG
---..((((((((..((((....)))).))))))))....((..((....(((..(((((.....)))))..))).))..((((..(((...............)))..)))))). ( -35.26, z-score =  -1.51, R)
>consensus
___CGGGAUGGUGGAGCGAUCAUUCGCACUCCAUCUGUUGCCGAGCGGAAGAAGAUUGCGGCAAACACAAAAUUCACCGAAGUAGGACUGAAUGUGAAGGUGAAUG__________
.........((.(((((((....))))))))).(((((......))))).(((..(((((.....)))))..)))......................................... (-16.38 = -16.38 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	203,424 – 203,543
Length	119
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	53.38
Shannon entropy	0.73869
G+C content	0.50983
Mean single sequence MFE	-30.88
Consensus MFE	-13.57
Energy contribution	-13.07
Covariance contribution	-0.50
Combinations/Pair	1.45
Mean z-score	-0.87
Structure conservation index	0.44
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.75
SVM RNA-class probability	0.805829
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 203424 119 + 204112
GGUGCGAUCAUUCGUACUCCUUCGGUUGGAGAGCUGCAGAAGGUGAUGGCAUCGAAAAGAUUCGCAGAACUUGGACUGAAUGUGGCACGGAACGCGGCCGAGAAGCCGAAGGUCAUAGU
(((((((....)))))))..(((((((.(((..((((....((((....))))(((....)))))))..))).)))))))((((((.(......((((......))))..))))))).. ( -40.70, z-score =  -1.30, R)
>dp4.Unknown_singleton_2130 3982 91 + 5907
---GUGAUUAUUCGCACUCCAUCUGUUGCCGAGCGGAAGAAAAUUGCGGAAAAUGCAAAGUUUGAUGAGGUAGGACUGACUGUGAAGGUCAAUG-------------------------
---.(((((.((((((.((..(((..((((...((...(((..(((((.....)))))..)))..)).)))))))..)).)))))))))))...------------------------- ( -22.60, z-score =  -0.82, R)
>droPer1.super_92 115746 91 - 190782
---GCGAUUAUUCGCACCCCUUCAGUGAGCGAACUGAGGAAGGUAGUGGCCAGCAGCAAAUUUACCGAAGCAGGACUGGAGGUUAAGAAGAGUC-------------------------
---((((....))))...((((((((.......(((.....(((((..((.....))....)))))....))).))))))))............------------------------- ( -23.80, z-score =  -0.48, R)
>droGri2.scaffold_15056 30759 116 - 38174
---GCGAUCAUUCGCACACCAUCUGUUGCCGAGCGGAAGAAGAUUGCGGGGAACGCAAAAUUCAGCGAAGUUGGUCUGGAAGUGAGUGUGAAAGAGAGACUGGGGCCGAAAGUGGUCGU
---((((((((((((......((((((....)))))).(((..(((((.....)))))..))).))))..(((((((...(((.....(....)....))).)))))))..)))))))) ( -36.40, z-score =  -0.86, R)
>consensus
___GCGAUCAUUCGCACUCCAUCUGUUGCCGAGCGGAAGAAGAUUGCGGCAAACACAAAAUUCACCGAAGUAGGACUGAAUGUGAAGGUGAAUG_________________________
...((((....))))..(((.(((((......))))).(((..(((((.....)))))..))).........)))............................................ (-13.57 = -13.07 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:02:19 2011